Department of Aquatic Animal Health Mangement, Bioinformatics Centre, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore, 575 002, India.
Curr Microbiol. 2021 May;78(5):2015-2024. doi: 10.1007/s00284-021-02472-2. Epub 2021 Apr 3.
Klebsiella pneumoniae, an opportunistic pathogen found in the environment and human mucosal surfaces, is a leading cause of nosocomial infections. K. pneumoniae is now considered a global threat owing to the emergence of multidrug-resistant strains making its infections untreatable. In this study, 254 strains of K. pneumoniae were screened for the presence of prophages using the PHASTER tool. Very few strains lacked prophages (3.1%), while the remaining harboured both intact (811) and defective prophages (709). A subset of 42 unique strains of K. pneumoniae was chosen for further analysis. Our analysis revealed the presence of 110 complete prophages which were further classified as belonging to Myoviridae (67.3%), Siphoviridae (28.2%) and Podoviridae family (4.5%). An alignment of the 110 complete, prophage genome sequences clustered the prophages into 16 groups and 3 singletons. While none of the prophages encoded for virulence factors, 2 (1.8%) prophages were seen to encode for the antibiotic resistance-related genes. The CRISPR-Cas system was prevalent in 10 (23.8%) out of the 42 strains. Further analysis of the CRISPR spacers revealed 11.42% of the total spacers integrated in K. pneumoniae chromosome to match prophage protein sequences.
肺炎克雷伯菌是一种环境和人体黏膜表面的机会性病原体，是医院获得性感染的主要原因。由于出现了多药耐药株，使感染无法治疗，肺炎克雷伯菌现在被认为是一种全球性威胁。在这项研究中，使用 PHASTER 工具筛选了 254 株肺炎克雷伯菌是否存在噬菌体。很少有菌株缺乏噬菌体（3.1%），而其余的则同时存在完整的（811）和有缺陷的噬菌体（709）。选择了 42 株独特的肺炎克雷伯菌亚系进行进一步分析。我们的分析显示存在 110 个完整的噬菌体，进一步分为肌尾噬菌体科（67.3%）、长尾噬菌体科（28.2%）和短尾噬菌体科（4.5%）。110 个完整噬菌体基因组序列的比对将噬菌体聚类为 16 个群和 3 个单倍体。虽然没有一个噬菌体编码毒力因子，但有 2 个（1.8%）噬菌体被发现编码与抗生素耐药性相关的基因。CRISPR-Cas 系统在 42 株中的 10 株（23.8%）中很常见。对 CRISPR 间隔区的进一步分析显示，总间隔区的 11.42%整合到肺炎克雷伯菌染色体中与噬菌体蛋白序列匹配。
